Stagonospora nodorum Database
Data site retirement
On 4/30/16 the Broad's Institute Stagonospora nodorum database and web site will be retired due to expiration of funding. For many years we have been pleased to work closely with the research community to create and support this resource. Genomic data can still be accessed in Genbank.
The Stagonospora nodorum (Phaeosphaeria nodorum) sequencing project is part of the Broad Institute Fungal Genome Initiative. Its goal was to release an annotated assembly with 10X genome sequence coverage for Stagonospora nodorum strain SN15.
The Stagonospora nodorum genome project represents a partnership between the Broad Institute and the International Stagonospora nodorum Genomics Consortium (IGGR).
This Sequencing Project was funded by the Australian Grains Research and Development Corporation and coordinated by the Australian Centre for Necrotrophic Fungal Pathogens. See Grains Research and Development Corporation (GRDC) for further information.
The main collaborator of Stagonospora nodorum genome project is:
Dr. Richard Oliver at Curtin University, Kent Street, Bentley, WA, 6102
The Eli and Edythe L. Broad Institute is a partnership among MIT, Harvard and affiliated hospitals and the Whitehead Institute for Biomedical Research. Its mission is to create the tools for genomic medicine and make them freely available to the world and to pioneer their application to the study and treatment of disease.
Our specific aims were as follows:
- Generate and assemble sequence reads yielding 10X coverage of the S. nodorum genome through whole genome shotgun sequencing.
- Perform automated annotation of the sequence assembly.
- Distribute the sequence assembly and results of our annotation and analysis. through a freely accessible, public web server at the Broad and by deposition of the sequence assembly in GenBank.
We produced whole genome shotgun sequence from two plasmid libraries (4kb and 10kb inserts) and a Fosmid library. The resulting >10X assembly was made public on 4/15/2005, and the results of automated genome annotation was made public 5/13/2005 and updated on 5/6/2011.
Questions about the project should be directed to firstname.lastname@example.org.
What is Stagonospora nodorum?
Stagonospora nodorum is a filamentous ascomycete that is a major pathogen of wheat and related cereals. It is also known as Septoria nodorum and the disease is variously called glume blotch and Septoria (or Stagonospora) nodorum blotch (not to be confused with Septoria leaf blotch which is caused by Mycosphaerella graminicola). The sexual stage is important in the field and the teleomorph is called Phaeosphaeria nodorum.
Stagonospora causes major losses in wheat crops. In Australia, losses of $57M pa are considered typical. Almost all these losses are concentrated in the Western Australian wheat belt. It is a major pathogen in most other wheat growing regions. In some areas, such as parts of eastern, it renders wheat an uneconomic crop.
Stagonospora is a member of the Dothideomycetes, a class of fungi that includes many important plant pathogens such as Leptosphaeria, Ascochyta, Pyrenophora, Cochliobolus, Alternaria and Mycosphaerella. It is the first Dothideomycete genome sequence to be publicly released.
The lifecycle of Stagonospora comprises both sexual and asexual phases. The asexual spores are released from pycnidia and rain-splashed to initiate new infection foci. The pycnidiospores germinate on the surface of the leaf and penetrate through stomata and directly through the epidermal cell walls. Cell wall penetrations are often associated with simple swollen hyphopodia. Once inside, hyphae grow through the leaf blade. After a few days and when the leaf cells have largely collapsed, pycnidia are formed to complete the life cycle.
The macroscopic symptoms are lens-shaped lesions in which brown pycnidia develop in appropriate conditions. Lesions often form in stem nodes, hence the name "nodorum". The most damaging aspect of the disease is infection of the head, leading to the glume blotch symptoms. Sexual development takes place on stubble and takes several months. The fungus is heterothallic. Ascospores are released from pseudothecia and spread on the wind. Seed-borne transmission is also important. Stagonospora can be easily cultured in vitro on simple defined media. Gene manipulation techniques including gene replacement have been developed and are relatively straightforward. However, sexual crossing in the laboratory is problematic.
Pathogenicity has been studied through the analysis of the effects of disrupting the expression of a number of genes. A picture is emerging whereby pathogenicity is seen to be a tightly regulated process in which the fungus battles the plant to maximise both the speed and quantity of sporulation.
Stagonospora nodorum is both an important pathogen in its own right and a model for the dothideomycetes. The aim of the genome sequencing is to provide the community with the tools to analyse and dissect the genetic basis of pathogenicity. The goal is to understand the function of genes controlling all aspects of pathogenicity. This will lead to novel control methods, based on improved understanding of the lifecycle of the pathogenicity, new targets for chemical control and methods of enhanced plant defence.
The haploid genome size of S. nodorum is estimated from the assembled genome sequence to be 37.1Mb. Pulsed field electrophoresis results have indicated that the genome comprises 14-19 chromosomes ranging from 0.4 to 3.5Mb. Strains differ markedly in their karyotype. This even applies to the progeny of a single ascus.
This Sequencing Project has been funded by the Australian Grains Research and Development Corporation and coordinated by the Australian Centre for Necrotrophic Fungal Pathogens. See the Grains Research & Development Corporation page for further information.
Stagonospora nodorum sn15 Annotation Update 2011-05-06
Of the 15990 predicted gene models, there are 14 mitochondrial transcripts, 12380 transcripts with experimental validation of some kind, and 3596 transcripts without validation. We consider the 12380 transcripts to be close approximation of the final list of genes in SN15 and should be used in comparisons with other species.
Those nuclear-encoded genes that have experimental validation have version number '3', eg: SNOG_16596.3 Those without validation have version numbers '1' or '2', eg: SNOG_06694.1 Mitochondrial genes have no version numbers, eg: mt_tRNA-Ile1
Citations for these updated gene sets:
- HANE JK, LOWE, RGT, SOLOMON, PS, TAN K-C, SCHOCH, CL, SPATAFORA, JWB, CROUS, PC, KODIRA, C, BIRREN, BW, GALAGAN, JE, TORRIANI, SFF, MCDONALD, BA & OLIVER (2007) Dothideomycete-plant interactions illuminated by genome sequencing and EST analysis of the wheat pathogen Stagonospora nodorum. Plant Cell 19: 3347-3368.
- BRINGANS S, HANE, JK, CASEY T, TAN K-C, LIPSCOMBE R, SOLOMON PS & OLIVER RP (2009) Deep proteogenomics; high throughput gene validation by multidimensional liquid chromatography and mass spectrometry of proteins from the fungal wheat pathogen Stagonospora nodorum BMC Bioinformatics 10 301.
- CASEY T, SOLOMON PS, BRINGANS S, TAN K-C, OLIVER RP & LIPSCOMBE R (2010) Quantitative proteomic analysis of G-protein signalling in Stagonospora nodorum using isobaric tags for relative and absolute quantification. Proteomics 10 38-47
- Oliver and Syme, personal communication.